title: Rb1L/L_1

city: London

first: Fred

last: Dick

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

data_processing:
Basecalls were performed in BaseSpace using the FASTQ generation application, version 1.0.0.
For alignment of reads to the mm9 genome, STAR v2.5.0a was used {Dobin, 2013 #840}.
To generate a genome index, the mm9 chromFa.tar.gz file was downloaded from UCSC to create mm9_full_genome.fa, and the following command was used: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir <STAR_genome_indices_directory> --genomeFastaFiles mm9_full_genome.fa --genomeSAsparseD 2 --limitGenomeGenerateRAM 20000000000 {Mouse Genome Sequencing, 2002 #841}.
For the alignments, the following STAR command was used: STAR --runMode alignReads --runThreadN 8 --genomeDir <STAR_genome_indices_directory> --readFilesIn <reads>.fastq --sjdbGTFfile mm9_UCSC_knownGene.gtf --sjdbOverhang 149 --sjdbInsertSave All --outSAMtype BAM Unsorted SortedByCoordinate --outFileNamePrefix <output> --outReadsUnmapped Fastx --outMultimapperOrder Random --outSAMattributes NH HI AS NM XS --outWigType wiggle.
StringTie v1.3.2 was then used to assemble RNA-Seq alignments into potential transcripts with the following command: stringtie <STAR_aligned_sample>.sortedByCoord.out.bam -o <output>.gtf -p 4 -G mm9_UCSC_knownGene.gtf -A <output>_gene_abund.tab -B -e {Pertea, 2015 #842}.
The prepDE.py script provided with StringTie was then utilized to extract read count information from the generated files and DESeq2 was used to determine differential gene expression between Rb1+/+ and Rb1L/L genotypes
Genome_build: mm9
Supplementary_files_format_and_content: Raw counts of sequencing reads aligning to genes (UCSC gene IDs used). Data is formatted as a matrix.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were prepared and cultured from E13.5 embryos according to previously reported methods (Hurford et al. 1997). Breifly, MEFs were grown in DMEM supplimented with 10% FBS, 2 mM L-glutamine, 50U/mL penicillin and 50 ug/ml streptomycin until passage 4.

extract_protocol:
Total RNA from proliferating MEFs was isolated using TRIzol reagent according to the standard protocol (Invitrogen).  All samples were further processed and sequenced at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca). Total RNA samples were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) and the RNA 6000 Nano kit (Caliper Life Sciences). Samples were then processed using the ScriptSeq Complete Gold Kit (H/M/R) (Illumina Inc.) which includes Ribo-Zero rRNA removal.
Samples were fragmented, cDNA was synthesized, tagged, cleaned-up and subjected to PCR with indexed reverse primers (ScriptSeq Index PCR Primers) to permit equimolar pooling of samples into one library.

tag: passage

value: Proliferating passage 4

value: E13.5 MEFs

tag: material

value: rRNA-depleted total RNA


title: Rb1L/L_3

status: Public on Nov 04 2019

type: SRA

state: ON

country: Canada

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype/variation


title: Mouse 0 h retina 1

city: Irvine

first: Les

last: Kallestad

state: CA

address: 829 Health Sciences Rd

department: Ophthalmology

country: USA

institute: University of California Irvine

data_processing:
Raw files were aligned using RNA-STAR
Rsubread's featurcounts was used to generate read counts
edgeR was used for DE
R enviroment was used to analyze data
Genome_build: GRCm38.p6 and Panu_3.0
Supplementary_files_format_and_content: csv, raw counts from Rsubread

molecule: polyA RNA

source_name: Mouse retina

extract_protocol:
Retina/RPE was isolated, stored at 4 degress in RNA later or RNA protect, respectively, and RNA was harvested miRNAeasy micro.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: gender

value: Male

tag: age

value: 30 days

tag: pmi interval

value: 0 h

tag: tissue

value: retina


title: elba2IgG_ChiP-seq

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

library_source: genomic

data_processing:
ChIP-seq: The ChIP-seq samples were mapped to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic.  For each of the four factors, the peak calling was performed by the ChIP-seq reads of wt or a mutant condition to its own mutant ChIP or IgG or Input. The peaks were called using MACS2 (Zhang et al. 2008) with default parameters and the confident peaks were determined by an FDR < 1%. The peaks overlapped with Drosophila blacklist were also removed.
ChIP-nexus: Before aligning the ChIP-nexus reads to the genome, the 5’ fixed barcode (1-5) was first removed and the random 4nt barcode was retained for each read. After the 3’ adaptor trimming by Trimmomatic, the sequencing reads were collapsed to only include unique reads. The random 4nt barcode was further removed and the reads with at least 22nt were retained for mapping. We mapped the reads using bowtie with the parameter setting “-k 1 -m 1 -v 2 --best --strata”. Similar to the ChIP-seq data, the ChIP-nexus peak calling was performed by MACS2 using the default parameter.
PRO-seq: The adaptors were first trimmed from the sequencing reads by cutadapt software and the reads with at least 15 nt were retained.  We then removed reads that mapped to rRNAs and the remaining reads were further mapped to the Drosophila melanogaster (dm3) genome assembly using BWA with the default parameters.
RNA-seq: After trimming the adaptor sequences using Trimmomatic, for each factor, the RNA-seq reads from the replicated wild type (x3) and mutant samples (x3) were mapped to the Drosophila melanogaster (dm3) genome assembly genome assembly using HISAT2.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig for coverage, bigbed for ChIP-seq/ChIP-nexus peak calls, RNA-seq #reads per gene in xlsx.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila early embryo

growth_protocol: Drosophila embryos were aged to 2-4 hours at 25 degrees and collected

extract_protocol:
Standard protocols were used to make chromatin extract for ChIP. Total RNAs were extracted with Trizol reagent for RNA-seq. Standard PRO-seq protocol was used to make PRO-seq libraries
ChIP-seq libraries were made using NEB DNA library prep kit. ChIP-nexus library was made as previouly described (He, et al ,2015). RNA-seq libraries were made by using illumina True-seq total RNA library kit LT. PRO-seq libraries were made as previously described (Kwak, et al, 2013).

value: elba2 mutant

value: early embyro

value: 2-4 hours

tag: molecule subtype

value: ChIPed genomic DNA

tag: antibody

value: IgG control in ChIP


title: Rb1L/L_2


title: wtInsv_ChiP-seq

value: yw

value: Insv antibody in ChIP


title: Rb1+/+_3


title: Rb1+/+_2


title: wtElba2_ChiP-seq

value: Elba2 antibody in ChIP


title: wtElba3_ChiP-seq

value: Elba3 antibody in ChIP


title: wtElba1_ChiP-seq

value: Elba1 antibody in ChIP


title: Rb1+/+_1

value: Proliferating passage 4


title: insvElba3_ChiP-seq

value: insv mutant


title: elba3IgG_ChiP-seq

value: elba3 mutant


title: dL_TFIIIC_1_ChIP

description: P4 MEFs formaldehyde fixed fixed prior to chromatin harvest

data_processing:
Basecalls were performed in BaseSpace using the FASTQ generation application, version 1.0.0.
ChIP-seq reads aligned using Bowtie2 version 2.3.0 using options -t -p 4 -D 15 -R 2 -L 32 -i S,1,0.75 -x  mm9 –U <reads>.fastq -S <output>.sam
Peaks were identified using MACS version 1.4.0rc2 according to the following options: –t <ChIP>.sam -c <input>.sam -n <output> -g mm -B -S.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain peaks that were found in each sample using the MACS data processing step

source_name: embryonic fibroblast chromatin

extract_protocol:
ChIP was conducted according to protocols adapted from Cecchini et al., 2014. Briefly, asynchronously cycling cells were fixed in either 1% formaldehyde in 1X PBS or in 2mM ethylene glycol bis(succinimidyl succinate (EGS) in 1X PBS followed by 1% formaldehyde. Both fixing reactions were neutralized with 0.125M glycine. Cross-linked chromatin was sonicated so most chromatin was ≤400 bp. Sheared chromatin was then normalized between experimental groups and pre-cleared with protein G Dynabeads and IgG. Pre-cleared chromatin was then incubated with protein G Dynabeads and ChIP antibodies to immunoprecipitate proteins.
Libraries were constructed according to the NEBNext Ultra II DNA library prep kit.

value: E13.5 MEFs

value: TFIIIC-220 (Bethyl, A301-291A)


title: dL_TFIIIC_2_ChIP


title: WT_TFIIIC_2_ChIP

value: wild type


title: insvInsv_ChiP-seq


title: MS_3new_S127

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Total RNA

data_processing:
Illumina Casava2.17 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using STAR v2.7.1a with parameters  --outSAMunmapped Within --outSAMattributes Standard --quantMode TranscriptomeSAM
Normalized counts for the genes were obtained using DEseq2 Bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include normalized counts for each Sample.

source_name: aBNST - total RNA

extract_protocol:
aBNST was homogenized in polysome buffer and RiboTag RNA pulled down using anti-HA coupled protein G beads. RNA was extracted with RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aBNST

value: 4 months


title: WT_TFIIIC_1_ChIP


title: insvElba1_ChiP-seq

value: early embyro


title: MS_2new_S127

description: RiboTag RNA

source_name: aBNST - RiboTag RNA


title: elba3Insv_ChiP-seq

value: 2-4 hours


title: MS_1new_S127

description: Total RNA


title: Rb1L/L 2

type: RNA

hyb_protocol: 5.5 ug of end-labeled cDNA was hybridized for 16 hours at 45°C on GeneChip Mouse Gene 1.0 ST Arrays that were subsequently washed and stained by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G using Command Console v3.2.4.

data_processing: RMA expression values derived from CEL files were log transformed prior to ANOVA analysis using Partek Genomics Suite.

label: biotin

label_protocol: RNA extracted from MEF pairs were used to biotin end-labeled single strand cDNA with the Affymetrix GeneChip WT PLUS Reagent Kit.

extract_protocol: Total RNA from proliferating MEFs was isolated using TRIzol reagent according to the standard protocol (Invitrogen).


title: elba3Elba3_ChiP-seq

value: ChIPed genomic DNA


title: dL_CAPH2_ChIP

description: P4 MEFs EGS and formaldehyde fixed fixed prior to chromatin harvest

value: CAP-H2 (Bethyl, A302-275A)


title: Rb1+/+ 2


title: MS_4new_S127

description: RiboTag RNA


title: Fasted mice, REP 1

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Normalized expression signals from Affymetrix CEL files were calculated using the Robust Multi-array Average algorithm (RMA), with the Affymetrix Expression Console Software (version 1.3.1.187)

source_name: Fasted mice, REP 1

label_protocol: Affymetrix protocol

extract_protocol: Nine mice per conditions were processed and RNA concentration and integrity were assessed with a NanoDrop® ND-1000 spectrophotometer and a Fragment Analyzer (Advanced Analytical Technologies, Ankeny, USA). Similar amounts of RNA from 3 different mice from the same condition were pooled prior to amplification and hybridization to the Affymetrix mouse gene 1.0 St array.

value: Liver

tag: genotype

value: Wild type

value: 12-14 weeks


title: Rb1+/+ 3


title: Refed mice, REP 3

source_name: Refed mice, REP 3


title: insvElba2_ChiP-seq

value: Elba2 antibody in ChIP


title: Rb1L/L 3


title: Rb1+/+ 1


title: Fasted mice, REP 2

source_name: Fasted mice, REP 2


title: RNA-seq, wild-type 7

description:
Liver homogenate of wild-type refed mice
WT_tot_7

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus.GRCm38.86 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012).Reads were also aligned to the Mus musculus.GRCm38.86 (Mm10) transcriptome using STAR (v. 2.5.2b, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Library sizes were scaled using TMM normalization (EdgeR package version 3.14.0; Robinson et al. 2010) and log-transformed with limma voom function (Limma package version 3.28.21 ; Law et al. 2014).Normalized data was corrected for batch effect using removeBatchEffect function (limma). Then, unwanted variation was removed using RUVr (RUVseq package version 1.6.2; Risso et al. 2014).
Differential expression was computed with limma (Ritchie et al. 2015) by fitting all samples into one linear model. Batch and RUVr-computed factors was added into the design matrix. Maf1 KO mice were compared to WT mice using moderated t-test for each contrast. The result files contain one row per gene. Columns contain the log2 average expression across all samples in the model (AveExpr), the log2 average expression of each condition tested (AveExp<>), the log fold change (logFC), the t (t), the p-value of the test (P.Value), the adjusted p-value computed by the Benjamini-Hochberg method, controlling for false discovery rate (FDR or adj.P.Val) and the antilog of the log fold-change (Fold_Change).
Genome_build: UCSC Mm10

source_name: Liver

extract_protocol:
Livers perfused with phosphate buffered saline (10-30 mg pieces) were added to 1 ml of TRIzol (Life Technologies), mechanically homogenized and RNA was extracted according to the manufacturer's instructions.
RNA concentration was determined with a NanoDrop®ND-1000 spectrophotometer and RNA quality was assessed with the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, USA). Libraries were prepared with the TruSeq Stranded Total RNA Ribo-Zero Globin kit according to the manufacturer’s instructions. Sequencing libraries were loaded onto one lane of a HiSeq 2000 flow cell and sequenced at 100 cycles.

treatment_protocol: Mice were fed a chow diet ad libitum until 12-14 weeks of age. Prior to sacrifice, mice were fasted overnight and then refed for four hours.

tag: experiment

value: RNA-seq

tag: age (weeks)

value: wild-type


title: Rb1L/L 1


title: RNA-seq, wild-type 6

description:
Liver homogenate of wild-type refed mice
WT_tot_6


title: dL_CAPD3_ChIP

value: Proliferating passage 4

value: CAP-D3 (in-house, affinity-purified rabbit Ab)


title: RNA-seq, wild-type 5

description:
Liver homogenate of wild-type refed mice
WT_tot_5


title: elba3Elba2_ChiP-seq

value: elba3 mutant


title: dL_H3K27me3_2_ChIP

value: E13.5 MEFs

value: H3K27me3 (EMD Millipore, 07-449)


title: Fasted mice, REP 3

source_name: Fasted mice, REP 3


title: RNA-seq, wild-type 3

description:
Liver homogenate of wild-type refed mice
WT_tot_3


title: dL_H3K27me3_1_ChIP


title: elba3Elba1_ChiP-seq

value: Elba1 antibody in ChIP


title: RNA-seq, wild-type 2

description:
Liver homogenate of wild-type refed mice
WT_tot_2


title: Refed mice, REP 2

source_name: Refed mice, REP 2


title: RNA-seq, wild-type 1

description:
Liver homogenate of wild-type refed mice
WT_tot_1


title: WT_CAPH2_ChIP

value: wild type


title: elba2Insv_ChiP-seq

value: elba2 mutant

value: early embyro

value: Insv antibody in ChIP


title: RNA-seq Maf1 total KO 5

description:
Liver homogenate of Maf1 KO refed mice
KO_tot_5

value: Maf1 KO


title: Refed mice, REP 1

source_name: Refed mice, REP 1

value: Liver


title: elba2Elba3_ChiP-seq

value: 2-4 hours

value: ChIPed genomic DNA

value: Elba3 antibody in ChIP


title: RNA-seq Maf1 total KO 4

description:
Liver homogenate of Maf1 KO refed mice
KO_tot_4

value: RNA-seq


title: RNA-seq Maf1 total KO 3

description:
Liver homogenate of Maf1 KO refed mice
KO_tot_3


title: RNA-seq, wild-type 4

description:
Liver homogenate of wild-type refed mice
WT_tot_4

value: wild-type


title: RNA-seq Maf1 total KO 2

description:
Liver homogenate of Maf1 KO refed mice
KO_tot_2


title: WT_H3K27me3_2_ChIP

value: Proliferating passage 4


title: elba2Elba2_ChiP-seq

value: Elba2 antibody in ChIP


title: WT_CAPD3_ChIP

value: CAP-D3 (in-house, affinity-purified rabbit Ab)


title: elba1Insv_ChiP-seq

value: elba1 mutant


title: RNA-seq Maf1 total KO 1

description:
Liver homogenate of Maf1 KO refed mice
KO_tot_1


title: INPUT, wild-type, fasted

description: Liver homogenate of wild-type mice fasted for 8 hours

data_processing:
Alignment : Tags from both Mouse and human DNA with perfect matches were directly extracted from the eland_extended mode of ELAND (v2e in the Illumina CASSAVA pipeline version 1.82) output, as previously described (Bonhoure et al, 2014).
Alignment : Tags with multiple matches were mapped onto the Mouse genome build Mm9 using the fetchGWI software and allowing 500 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches.
Pol III scores were calculated for bins including the annotated gene body ±150bp as the mean log2 (IPtag count/INPUTtag count) of two replicates per condition.
Genome_build: UCSC Mm9 and Hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
ChiP-seq was performed as described (Bonhoure et al., 2014)
Libraries were prepared with 12 ng of ChIP DNA (ChIP-seq) or genomic DNA (INPUT) according to manufacturer's's instruction with the ChIP-seq DNA Sample prep kit” (Illumina, 1003473)

tag: chip antibody


title: INPUT, wild-type, refed

description: Liver homogenate of wild-type refed mice


title: WT_H3K27me3_1_ChIP

value: E13.5 MEFs

value: H3K27me3 (EMD Millipore, 07-449)


title: INPUT, Maf1 KO, refed

description: Liver homogenate of Maf1 KO refed mice


title: elba2Elba1_ChiP-seq

value: Elba1 antibody in ChIP


title: INPUT, Maf1 KO, fasted

description: Liver homogenate of Maf1 KO mice fasted for 8 hours


title: ChIP-seq Rpc4, Maf1 KO, fasted, rep2

value: anti-Rpc4 (Bonhoure et al, 2014)


title: dL_input_TFIIIC_2

description: P4 MEFs formaldehyde fixed fixed prior to chromatin harvest


title: elba1_Input

value: early embyro

value: Input control in ChIP


title: dL_input_TFIIIC_1


title: elba1Elba3_ChiP-seq


title: ChIP-seq Rpc4, wild-type, fasted, rep2


title: elba1Elba2_ChiP-seq


title: WT_input_TFIIIC_2

value: wild type


title: ChIP-seq Rpc4, wild-type, fasted, rep1


title: elba1Elba1_ChiP-seq


title: ChIP-seq Rpc4, wild-type, refed, rep2


title: WT_input_TFIIIC_1


title: ChIP-seq Rpc4, Maf1 KO, refed, rep2

description: Liver homogenate of Maf1 KO refed mice

value: Maf1 KO


title: ChIP-seq Rpc4, Maf1 KO, refed, rep1

description: Liver homogenate of Maf1 KO refed mice


title: EG001_OM_Adipocytes_RNASeq_1_Rep_884_2

city: Kansas City

first: Elin

last: Grundberg

state: Missouri

address: 2401 Gillham Road

institute: CHILDREN'S MERCY HOSP (KANSAS CITY, MO)

description: HI.0884.002.Index_19.EG001_OM_Adipocytes_RNASeq_1_Rep

data_processing:
Raw reads were trimmed for quality (phred33 ≥30) and length (n≥32), and Illumina adapters were clipped off using Trimmomatic v. 0.35
Filtered reads were then aligned to the GRCh38 human reference using STAR v. 2.5.3a
Raw read counts of genes were obtained using htseq-count v.0.6.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file containing RPKM values of each sample

organism: Homo sapiens

source_name: Adipocytes from adipose tissue

extract_protocol:
Adipose tissue was digested with collagenase according to a modification of the Robdell method (Tchernof et al., 2006). Briefly, adipose tissue samples were digested with collagenase type 1 in Krebs-Ringer-Henseleit (KRH) buffer for 45 minutes at 37°C. Cell suspensions containing mature adipocytes and the stromal-vascular fraction (SVF) were then filtered with a nylon mesh and washed 3 times with KRH buffer. The nature of the buoyancy adipocytes allows them to float to the surface. Mature adipocytes were discarded and the remaining solution containing the SVF was centrifuged 1500 rpm for 5 minutes. The pellet was washed with pre-adipocyte growth medium (PGM) (DMEM-F12 supplemented with 10% calf serum, 1% penicillin-streptomycin, 17µM pantothenic acid, 33µM biotin, 100µM ascorbic acid and 2,5 µm/ml amphoB) followed by a second centrifugation. Cells were cryopreserved using freezing medium (PGM supplemented with 40% FBS and 10% DMSO). The medium was added to the pellet and was frozen with a temperature gradient (-1 °C/ minutes) and store at -80°C until analysis.
0.5 to 3 million cells were re-suspended in 500 uL TRIzol Reagent and total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA library preparations were carried out on 500 ng of RNA with RNA integrity number (RIN)>7 using the Illumina TruSeq Stranded Total RNA Sample preparation kit, according to manufacturer's protocol. Final libraries were analyzed on a Bioanalyzer and sequenced on the Illumina HiSeq

value: Adipocytes from visceral adipose tissue


title: ChIP-seq Rpc4, wild-type, refed, rep1


title: dL_input_H3K27me3_2

description: P4 MEFs EGS and formaldehyde fixed fixed prior to chromatin harvest


title: WT3_TOTL

description:
Total RNA fragments
Liver homogenate of wild-type refed mice

data_processing:
Sequence tags from RNA-seq and from ribosome footprints performed in parallel from the same sample were aligned to both the Drosophila melanogaster BDGP Release 6 + ISO1MT/dm6 and Mus musculus NCBI37/mm9 genome assemblies, common tags were eliminated, the remaining tags were then aligned onto the dm6 and mm9 CDSs (in a first step, without any mismatch allowed, and in a second step with up to one mismatch allowed), then all aligned tags were remapped and their position on genes recorded.
Tags aligning to regions encoding rRNA or scRNAs were eliminated, and the remaining aligned tags were normalized i) to the total number of aligned sequence tags in each experiment, and ii) with TMM from EdgeR. Transcripts with less than 20 reads in total RNAseq for all replicates were discarded.
A correction factor calculated from the signal of the Drosophila S2 Schneider cell spike material was then applied to the normalized tag numbers (log2) to obtain scores for individual transcript types. The average of the scores for all transcripts derived from a single gene (with different TSSs, splicing patterns, or poly A addition sites) was then calculated to obtain the RNA-seq-normalized tag numbers (RNA-seq-NTC) and the ribosome footprint normalized tag counts (RF-NTC)
Genome_build: UCSC Mm9 and DM6
Supplementary_files_format_and_content: Matrix table with transcripts scores for each condition

extract_protocol:
Livers were collected from 12 week-old mice. Mice were sacrificed at 9 PM and livers were directly lysed in the polysome buffer and kept on ice for 10 min. Samples were centrifuged at 3000 rpm during 3 min and the supernatants were used for library preparation. Similar material extracted from Drosophila S2 cells was used as a spiking control and added to the mouse material at a ratio of 1/15. Thirty OD of the spiked material was used for library preparation.
Libraries of Ribo-seq and total RNA-seq were prepared according to the Illumina TruSeq Ribo Profile Mammalian protocol. The Truseq Ribo profile Nuclease was replaced by the RNase I from Ambion (Cat N. AM2295) to generate the ribosome footprinting.


title: EG001_OM_Adipocytes_RNASeq_1_884_1

description: HI.0884.001.Index_12.EG001_OM_Adipocytes_RNASeq_1


title: EG001_OM_Adipocytes_RNASeq_1_884_2

description: HI.0884.002.Index_12.EG001_OM_Adipocytes_RNASeq_1


title: WT1_TOTL


title: ChIP-seq Rpc4, Maf1 KO, fasted, rep1


title: WT3_RPFL

description:
RNA from Ribosome footprinting
Liver homogenate of wild-type refed mice

data_processing:
Library strategy: Ribo-Seq
Sequence tags from RNA-seq and from ribosome footprints performed in parallel from the same sample were aligned to both the Drosophila melanogaster BDGP Release 6 + ISO1MT/dm6 and Mus musculus NCBI37/mm9 genome assemblies, common tags were eliminated, the remaining tags were then aligned onto the dm6 and mm9 CDSs (in a first step, without any mismatch allowed, and in a second step with up to one mismatch allowed), then all aligned tags were remapped and their position on genes recorded.
Tags aligning to regions encoding rRNA or scRNAs were eliminated, and the remaining aligned tags were normalized i) to the total number of aligned sequence tags in each experiment, and ii) with TMM from EdgeR. Transcripts with less than 20 reads in total RNAseq for all replicates were discarded.
A correction factor calculated from the signal of the Drosophila S2 Schneider cell spike material was then applied to the normalized tag numbers (log2) to obtain scores for individual transcript types. The average of the scores for all transcripts derived from a single gene (with different TSSs, splicing patterns, or poly A addition sites) was then calculated to obtain the RNA-seq-normalized tag numbers (RNA-seq-NTC) and the ribosome footprint normalized tag counts (RF-NTC)
Genome_build: UCSC Mm9 and DM6
Supplementary_files_format_and_content: Matrix table with transcripts scores for each condition


title: EG001_OM_Adipocytes_RNASeq_1_Rep_884_1

description: HI.0884.001.Index_19.EG001_OM_Adipocytes_RNASeq_1_Rep


title: WT1_RPFL


title: WT_input_CAPH2_CAPD3_H3K27me3_2


title: WT2_TOTL


title: WT2_RPFL


title: EG-027_IA_RNA_1_3740_4


title: WT_input_H3K27me3_1


title: KO4_TOTL

description:
Total RNA fragments
Liver homogenate of Maf1 KO refed mice


title: Cdca3_4_Rb1L/L

data_processing:
Library strategy: 4C-Seq
Sequence reads were first trimmed to 20 bp total after the primer and bait sequence (excluding the HindIII site) using the FASTQ trimmer from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
w4CSeq was then used to identify 4C sites, statistically significant regions, and look at intra- and inter-chromosomal interactions {Cai, 2016 #796}. For this analysis, the mm9 genome was used, 500 enzyme sites was selected as the bin size for trans chromosomes (size_inter), 100 enzyme sites was selected as the bin size for cis chromosomes (size_intra), 3000 enzyme sites was selected as the background window size for the cis chromosome (window_intra), and 0.05 was used as the FDR threshold.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file with all positive hits for bait regions with p-values listed in the 4th column (<name>_positive_hits.bed) and another bed file with final processed significant interacting regions in the genome (<name>_significant_regions.bed).

extract_protocol:
3C was conducted according to protocols adapted from Hagège et al. {Hagege, 2007 #809}. Briefly, cells were trypsinized, centrifuged and resuspended to make a single-cell suspension followed with crosslinking in 1% formaldehyde/10% FCS/PBS. The reactions were quenched with glycine and cells were then pelleted and lysed in 5 mL cold lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and protease inhibitors). Samples were digested with HindIII, ligated using T4 DNA ligase, samples were treated with proteinase K and cross-links were reversed at 65°C. To generate a 4C products, 3C products were processed according to protocols adapted from Splinter et al. {Splinter, 2012 #783}. Briefly, 3C products were digested with NlaIII, ligated with T4 DNA ligase, and purified.
Primers were designed for the bidirectional promoters of interest for inverse PCR reactions. For Illumina sequencing, all reading primers started with an Illumina read adapter sequence, 5’-AATGATACGGCGACCACCGAGATCTACACACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; followed by a unique tag 0-3 nucleotides in length. After the tag, the reading primers contained sequence unique to the viewpoint of interest, as close as possible to the HindIII digestion site. For the reverse sequencing primers for these viewpoints, the primers again started with an Illumina adapter sequence, 5’-CAAGCAGAAGACGGCATACGAGAT-3’; followed by sequence unique to the viewpoint of interest, close to the NlaIII restriction sites. 4C product for sequencing was then prepared using Expand Long Template Polymerase (Roche) and 3.2 µg of 4C template split between 16 PCR reactions. PCR reactions were pooled after completion and purified. 4C PCR products were then pooled equimolarly into one library.

tag: viewpoint

value: Cdca3/Usp5 bidirectional promoter

tag: mef pair id


title: KO4_RPFL

description:
RNA from Ribosome footprinting
Liver homogenate of Maf1 KO refed mice


title: Cdca3_4_Rb1+/+

tag: passage


title: EG-024_IA_RNA_1_3740_3


title: KO2_RPFL


title: KO2_TOTL


title: Cdca3_3_Rb1L/L


title: KO1_RPFL


title: KO1_TOTL


title: EG-023_IA_RNA_1_3740_3


title: dL_input_CAPH2_CAPD3_H3K27me3_1


title: Cdca3_3_Rb1+/+


title: EG-025_IA_RNA_1_3740_4


title: Cdca3_2_Rb1L/L


title: EG-021_IA_RNA_1_3740_3


title: EG-027_SC_RNA_1_3740_4

value: Adipocytes from subcutaneous adipose tissue


title: Cdca3_2_Rb1+/+


title: Cdca3_1_Rb1L/L


title: EG001_SC_Adipocytes_RNASeq_1_Rep_884_2

description: HI.0884.002.Index_6.EG001_SC_Adipocytes_RNASeq_1_Rep


title: shRNAseq_rep3_DOX_T15

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description:
shRNA screen
PCR-product (from genomic DNA)
processed data file:
shRNAseq_counttable.txt

data_processing:
Library strategy: shRNA screen
For shRNA screen analysis, fastq files were mapped to the Decipher-human-module-1 reference database containing all 18-nucleotide barcode-sequences that correspond to the almost 25700 individual shRNA sequences that are contained in the library Decipher_HumanModule1 (Cellecta). This reference sheet is attached as the supplementary file "Reference_barcode_sequences_Decipher_HumanModule1". Mapping was done using the Bacrode-Deconvoluter-Software (The Decipher Project; Cellecta) with default settings.
The counts of aligned reads for all replicates and conditions were combined in a count-table. Enrichment or depletion of shRNAs between two distinct screening-conditions was calculated using the publicly available Galaxy-based shRNAseq tool (edgeR-based statistics).
Genome_build: N/A
Supplementary_files_format_and_content: shRNAseq_counttable.txt: Count matrix containing an identifier that unambiguously identifies a barcode and corresponding shRNA sequence. Furthermore, this count matrix contains the counts of aligned reads for all shRNAs of all samples. This count table was used as input for the analyses with the tool shRNAseq.

source_name: SW480TetOnAPC cells

growth_protocol: SW480TetOnAPC cells were grown in RPMI 1640 (Sigma). All media were supplemented with 10% FBS (Sigma) and 1% penicillin/streptomycin (Sigma).

extract_protocol:
Genomic DNA was extracted from harvested cells using a cell-lysis buffer containing SDS and RNaseA. DNA was sheared by sonification and purified using a phenol-choroform extraction followed by an isopropanol precipitation.
To retrieve Decipher-18bp-barcode-sequences that have previously been integrated together with the shRNA sequences into the genomic host DNA via lentiviral transduction, custom PCR-primers were used that specifically bind to the pRSI9-Decipher vector at sequences flanking the shRNA-specific barcode sequence. In two subsequent PCRs, the barcode sequences were first recovered from the genomic DNA and second relevant adapter-sequences were introduced for hybridization of the PCR-products to the Illumina GAIIx Next-Generation-Sequencer following gel-purification and quantification and size determination using the Experion Automated Electrophoresis System (Bio-Rad).

treatment_protocol: SW480TetOnAPC cells were treated with 0.5 µg/ml doxycycline or ethanol.

value: human colorectal cancer cell line

tag: cell line

tag: treatment

value: DOX

tag: shRNA


title: shRNAseq_rep3_DOX_T0


title: Cdca3_1_Rb1+/+

value: Proliferating passage 4

tag: cell type

tag: genotype/variation


title: shRNAseq_rep3_ETOH_T15

value: EtOH


title: ExVivoBlood_PPLO_rep1

city: Wuhan

first: JIN

last: CHAO

state: Hubei

address: 1#, Shizishan Street

country: China

institute: Huazhong Agricultural University

description: Gene expression  after 7days in PPLO broth-incubated  calf's blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software  (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

source_name: Peripheral Blood, incubated with PPLO broth

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick Amp Labeling Kit  (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Lyse cells were homogenized in TRIzol Reagent by repetitive pipetting. RNA was prepared with phase separation with chloroform, precipitation with isopropyl alcohol, and washed with 75% ethanol and last redissolved. Total RNA clean-up was performed with RNasey Mini Kit(Qiagen p/n 74104), and RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each calf  was nasal inoculated with 10^9 CFU of HB0801 strain, or P150 strain respectively, in 5 mL of PPLO broth. The NC calve were mock inoculated with an equal volume of sterile PPLO broth. After 7 days post-incubated, PBMCs were isolated from blood samples on a Ficoll gradient,  washed with phosphate-buffered saline (PBS), and suspended in RPMI-1640 complete medium with 10% FBS with volumes equal to original blood samples. Then the PBMCs were inoculated in a 12-well plate at a density of 2-4 × 10^6 live cells each well, and co-incubated with 2μg for each well heat-killed either HB0801 or P150 M. bovis strains. The PBMCs from the NC group were added with correspond volume of sterile cell culture medium. After 72 h, the cells were harvested and disposed for microarray assay.

value: whole blood

value: PBMC

tag: gender

value: male

tag: age

value: < 1.5 month

tag: infection

value: control


title: EG001_SC_Adipocytes_RNASeq_1_884_1

description: HI.0884.001.Index_5.EG001_SC_Adipocytes_RNASeq_1

tag: tissue


title: shRNAseq_rep3_ETOH_T0


title: ExVivoBlood_PPLO_rep2


title: EG-022_IA_RNA_1_3740_3


title: EG001_SC_Adipocytes_RNASeq_1_Rep_884_1

description: HI.0884.001.Index_6.EG001_SC_Adipocytes_RNASeq_1_Rep


title: ExVivoBlood_P150_rep3

description: Gene expression  after 7days in M.bovis P150-infected  calf's blood

source_name: Peripheral Blood,infected with M.bovis P150

value: M.bovis P150


title: shRNAseq_rep2_ETOH_T15


title: shRNAseq_rep2_DOX_T0


title: Pole_4_Rb1+/+

source_name: Mouse embryonic fibroblasts

value: E13.5 MEFs

value: Pole/Pxmp2 bidirectional promoter


title: Pole_4_Rb1L/L


title: ExVivoBlood_PPLO_rep3


title: ExVivoBlood_HB0801_rep3

description: Gene expression  after 7days in M.bovis HB0801-infected  calf's blood

source_name: Peripheral Blood,infected with M.bovis HB0801

value: M.bovis HB0801


title: Pole_3_Rb1L/L


title: ExVivoBlood_P150_rep1


title: ExVivoBlood_P150_rep2


title: EG-026_SC_RNA_1_3740_4


title: shRNAseq_rep1_DOX_T15


title: ExVivoBlood_HB0801_rep2


title: ExVivoBlood_HB0801_rep1


title: shRNAseq_rep1_DOX_T0


title: EG001_SC_Adipocytes_RNASeq_1_884_2

description: HI.0884.002.Index_5.EG001_SC_Adipocytes_RNASeq_1


title: Pole_3_Rb1+/+


title: shRNAseq_rep1_ETOH_T15


title: Pole_2_Rb1L/L


title: shRNAseq_rep1_ETOH_T0


title: shRNAseq_rep2_DOX_T15


title: EG-024_SC_RNA_1_3740_4


title: Pole_2_Rb1+/+


title: RNAseq_APCres_rep2

description:
processed data file:
RNAseq_SW480_logFC.txt

data_processing:
For RNA-seq analysis, reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 (Langmead, 2010) using default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Reads per gene (Ensembl database GRCh37.p13) were counted with the "summarizeOverlaps" function in the R package {GenomicFeatures}.
Non- or weakly expressed genes were removed (threshold: mean read count per gene over all samples >1).
Differential gene expression was called using EdgeR and adjusting the calculated p-value with the Benjamini-Höchberg procedure.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file containing gene names, gene description, log2FC, log2CPM, p-value, Benjamini-Höchberg-adjusted p-value

extract_protocol:
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) including on-column digestion of DNA. Poly-A+ RNA was purified from total RNA with the NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB).
RNA sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.

treatment_protocol: SW480TetOnAPC cells were treated with 0.5 µg/ml doxycycline or ethanol for 48 hours to restore APC expression.

value: Dox


title: RNAseq_APCres_rep3


title: RNAseq_APCres_rep1


title: EG-023_SC_RNA_1_3740_3


title: EG-022_SC_RNA_1_3740_3


title: RNAseq_APCdef_rep1


title: RNAseq_APCdef_rep3


title: Pole_1_Rb1L/L


title: Pole_1_Rb1+/+


title: EG-021_SC_RNA_1_3740_3


title: EG-027_IA_SVF_RNA_1_3740_6

description: HI.3740.006.Index_23.EG-027_IA_SVF_RNA_1

source_name: SVF from adipose tissue

value: SVF from visceral adipose tissue


title: shRNAseq_rep2_ETOH_T0


title: RNAseq_APCdef_rep2

treatment_protocol: SW480TetOnAPC were treated with 0.5 µg/ml doxycycline or ethanol for 48 hours to restore APC expression.


title: EG-026_IA_SVF_RNA_1_3740_6

description: HI.3740.006.Index_25.EG-026_IA_SVF_RNA_1


title: EG-025_SC_RNA_1_3740_4


title: EG-024_IA_SVF_RNA_1_3740_5

description: HI.3740.005.Index_10.EG-024_IA_SVF_RNA_1


title: EG-022_IA_SVF_RNA_1_3740_5


title: EG-021_IA_SVF_RNA_1_3740_4

description: HI.3740.004.Index_12.EG-021_IA_SVF_RNA_1


title: Pemphigus vulgaris IP07 Sample52

city: Yokohama

first: Junshi

last: Yazaki

state: Kanagawa Prefecture

address: 1-7-22 Suehirocho, Tsurumi Ward,

country: Japan

institute: RIKEN

description:
4Oligos(Oligo59-62) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :106 dilution serum, PV patients 02 (D2) 4
Supplementary Table S8
52_18_S15_L001

data_processing:
The counting barcode region, which is a 30-bp semi-random sequence, was used to determine the molecule number after identifying each protein based on the 8-bp protein barcode sequence.
The fixed six bases in the counting barcode were used for filtering to exclude molecules with at least one mismatched fixed base from the molecule counting process.

organism: synthetic construct

source_name: 8Oligos_Supplementary Table S8 and Figure 4A

extract_protocol:
The barcoded DNA template was PCR-amplified as follows: 95°C for 2 min; followed by 4 cycles of 10 s at 95°C, 10 s at 60°C, and 1 min at 68°C; 25 cycles of 10 s at 60°C and 2 s 68°C of 1 min; and a final elongation step for 5 min at 68°C. The amplified DNA was purified by using Agencourt AMPure XP kit (Beckman) and the quality of the DNA library was assessed by Bioanalyzer (Agilent, USA), as recommended by the manufacturer. The amplified 174-bp products, including the Illumina adapter and index sequence, were analyzed by the MiSeq system (Illumina) with dual-indexed sequencing in a paired-end flow cell, to read 75 bp, including the amplified 38 bp of barcode DNA
HaloTag barcode-seq

tag: sample type

value: Pemphigus vulgaris IP07

tag: disease state

value: Pemphigus vulgaris


title: Pemphigus vulgaris IP03 Sample48

description:
4Oligos(Oligo59-62) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :106 dilution serum, Healthy 02 (H2)  3
Supplementary Table S8
48_10_S7_L001

value: Pemphigus vulgaris IP03


title: Pemphigus vulgaris IP04 Sample49

description:
4Oligos(Oligo75-78) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :106 dilution serum, Healthy 02 (H2)  3
Supplementary Table S8
49_14_S11_L001

value: Pemphigus vulgaris IP04


title: Pemphigus vulgaris IP08 Sample53

description:
4Oligos(Oligo75-78) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :106 dilution serum, PV patients 02 (D2) 4
Supplementary Table S8
53_22_S19_L001

value: Pemphigus vulgaris IP08


title: EG-027_SC_SVF_RNA_1_3740_6

description: HI.3740.006.Index_27.EG-027_SC_SVF_RNA_1

value: SVF from subcutaneous adipose tissue


title: Pemphigus vulgaris IP02 Sample47

description:
4Oligos(Oligo75-78) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :104 dilution serum, Healthy 01 (H1)  1
Supplementary Table S8
47_29_S26_L001

value: Pemphigus vulgaris IP02


title: Obesity_6

city: Shijiazhuang

first: Linlin

last: Yang

state: Hebei

address: 348, Heping west road

institute: Hebei General Hospital

description: Gene expression data from adipose tissue in control subject

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: The raw data were normalized by Expression Console.

source_name: Adipose tissue from control subject 6

label_protocol: After passing the quality control, total RNA was amplified, labeled and purified by Affymetrix WT PLUS Reagent Kit (Cat#902280, Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Per 100mg Adipose sample was homogenized in 1mL of RNAiso Plus by using a homogenizer. Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy microi kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: All adipose tissues were collected during cholecystectomy and immediately stored at -80°C. Whole transcriptome data was obtained by HTA2.0 microarray.

value: Visceral fat tissue


title: Pemphigus vulgaris IP01 Sample46

description:
4Oligos(Oligo59-62) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :104 dilution serum, Healthy 01 (H1)  1
Supplementary Table S8
46_25_S22_L001

value: Pemphigus vulgaris IP01


title: MDA-MB-231 cell clone 6 days + dox, control rep1

city: Heidelberg

middle: R

last: Berger

address: INF 581

institute: DKFZ

description: SAMPLE 5

hyb_protocol: Standard Illumina Hybridisation Protocol (Part # 11322355 Rev. A (Whole-Genome Gene Expression Direct Hybridisation Assay Guide))

scan_protocol: Standard Illumina Scanning Protocol (Part # 11322355 Rev. A (Whole-Genome Gene Expression Direct Hybridization Assay Guide))

data_processing: The data were normalized using quantile normalization. As test for significance the student’s t-test was used on the bead expression values of the two groups of interest (+dox and -dox). The average expression value was calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

source_name: Mammary breast adenocarcinoma cell line

label_protocol: Illumina TotalPrep-RNA Amplification (P/N IL1791M Revision C)

growth_protocol: The established cell clone was cultivated in appropriate media with or without doxycycline for 3 or 6 days.

extract_protocol: The RNA was isolated by RNeasy mini-kit (Qiagen) in accordance with the prescribed protocol provided with the kit. The quality control of the total RNA was performed with Agilent Bioanalyser.

tag: genotype

tag: time (mirna expression)

value: 6 days off


title: EG-026_SC_SVF_RNA_1_3740_6

description: HI.3740.006.Index_21.EG-026_SC_SVF_RNA_1


title: MDA-MB-231 cell clone 6 days - dox, OPN knockdown rep1

description: SAMPLE 7

value: miRNA mediated OPN knockdown

value: 6 days on


title: EG-023_IA_SVF_RNA_1_3740_5


title: Control 2

source_name: Adipose tissue from control subject 2


title: Pemphigus vulgaris IP06 Sample51

description:
4Oligos(Oligo75-78) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :104 dilution serum, PV patients 01 (D1) 5
Supplementary Table S8
51_5_S2_L001

value: Pemphigus vulgaris IP06


title: Control 3

source_name: Adipose tissue from control subject 3


title: Control 5

source_name: Adipose tissue from control subject 5


title: Control 1

source_name: Adipose tissue from control subject 1


title: MDA-MB-231 cell clone 6 days + dox, control rep2

description: SAMPLE 6

value: control


title: MDA-MB-231 cell clone 3 days - dox, OPN knockdown rep1

description: SAMPLE 3

value: 3 days on


title: MDA-MB-231 cell clone 6 days - dox, OPN knockdown rep2

description: SAMPLE 8


title: Obesity 5

description: Gene expression data from adipose tissue in obese patient

source_name: Adipose tissue from obese patient 5


title: Obesity 4

source_name: Adipose tissue from obese patient 4


title: Control 4

source_name: Adipose tissue from control subject 4


title: MDA-MB-231 cell clone 3 days + dox, control rep2

description: SAMPLE 2

value: 3 days off


title: MDA-MB-231 cell clone 3 days - dox, OPN knockdown rep2

description: SAMPLE 4


title: MDA-MB-231 cell clone 3 days + dox, control rep1

description: SAMPLE 1


title: negative control for IP12 Sample44

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 1018dilution human serum
Supplementary Table S7
44_31_S31_L001

source_name: 4Oligos_Figure 3C (green)

value: negative control for IP12


title: Highthroughput01 Sample45

description:
51Oligos(Oligo05-10,12-16,39-78) Supplementary Table S1
HaloTag barcoding highthrouput assay 01. 51 barcoded proteins for PPI sucreen of bZIP53 query on Halo magnetic beads
Supplementary Table S4
45_33_S33_L001

source_name: 51Oligos_Supplementary Table S4


title: EG-023_SC_SVF_RNA_1_3740_5


title: Pemphigus vulgaris IP05 Sample50

description:
4Oligos(Oligo59-62) Supplementary Table S1
Pemphigus vulgaris immunoprecipitation :104 dilution serum, PV patients 01 (D1) 5
Supplementary Table S8
50_1_S30_L001

value: Pemphigus vulgaris IP05


title: negative control for IP09 Sample41

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 1012 dilution human serum
Supplementary Table S7
41_27_S27_L001

value: negative control for IP09


title: Riboseq_RNA_APCres_shEIF2B5_rep3

description:
processed data file:
Riboseq_RNA_SW480_rep3.txt

data_processing:
Library strategy: Ribo-seq
For Ribo-seq experiments, reads were mapped against the human genome (HG38) using STAR (Dobin et al.) and processed using PRICE (under revision) based on annotations from Ensembl (v86). Briefly, a generative model was fitted per experiment to the observed positions of annotated codons in strongly translated ORFs. This increased signal-to-noise levels from about 3 to more than 5 when mapping reads to codons. Then, translated ORFs were determined by the generalized binomial test built into PRICE using all pooled samples, and each ORF was quantified per experiment using the number of reads mapped to its codons. For the corresponding RNA-seq, reads were mapped against the human genome (HG38) using STAR (Dobin et al.). Then, reads per gene were counted when they were consistent with at least one transcript annotated in Ensembl v86.
genome build: hg38
Supplementary_files_format_and_content: Content of Riboseq_RPF_SW480.txt is described in README.txt. .txt files of the corresponding RNA-seq contain Ensembl gene IDs and non-normalized fractional counts for multimapping genes.

source_name: SW480TetOnAPC cells

extract_protocol:
RNA sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) including on-column digestion of DNA. Poly-A+ RNA was purified from total RNA with the NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB).

treatment_protocol: SW480TetOnAPC cells were lentivirally infected with an shRNA targeting eIF2B5 or non-specific control (shLuciferase). Cells were treated with 0.5 µg/ml doxycycline or ethanol for 96 hours to restore APC expression.

value: human colorectal cancer cell line

value: Dox


title: negative control for IP08 Sample40

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 1012 dilution human serum
Supplementary Table S7
40_26_S26_L001

source_name: 4Oligos_Figure 3C (red)

value: negative control for IP08


title: EG-024_SC_SVF_RNA_1_3740_5

description: HI.3740.005.Index_11.EG-024_SC_SVF_RNA_1

value: SVF from subcutaneous adipose tissue


title: EG-021_SC_SVF_RNA_1_3740_5

description: HI.3740.005.Index_19.EG-021_SC_SVF_RNA_1


title: negative control for IP06 Sample38

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 108 dilution human serum
Supplementary Table S7
38_23_S23_L001

value: negative control for IP06


title: negative control for IP10 Sample42

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 1018 dilution human serum
Supplementary Table S7
42_29_S29_L001

source_name: 4Oligos_Figure 3C (blue)

value: negative control for IP10


title: negative control for IP07 Sample39

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 1012 dilution human serum
Supplementary Table S7
39_25_S25_L001

value: negative control for IP07


title: EG-022_SC_SVF_RNA_1_3740_5


title: negative control for IP05 Sample37

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 108 dilution human serum
Supplementary Table S7
37_22_S22_L001

value: negative control for IP05


title: negative control for IP04 Sample36

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 108 dilution human serum
Supplementary Table S7
36_21_S21_L001

value: negative control for IP04


title: Riboseq_RNA_APCres_shCTR_rep3

value: shCTR


title: negative control for IP11 Sample43

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 1018 dilution human serum
Supplementary Table S7
43_30_S30_L001

value: negative control for IP11


title: negative control for IP03 Sample35

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 104 dilution human serum
Supplementary Table S7
35_19_S19_L001

value: negative control for IP03


title: negative control for IP02 Sample34

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 104 dilution human serum
Supplementary Table S7
34_18_S18_L001

value: negative control for IP02


title: Healthy39 RNA-Seq

city: Rehovot

first: Dan

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq2.17 was used for basecalling.
Sequenced reads were trimmed from adaptor sequence, polyA/T sequences and low quality bases (quality score <10) at the beginning and end of all reads using cutadapt1.10. reads shorter than 30bp were discarded. Mapping to reference genome and TPM calculation were done using RSEM1.2.18 (Li and Dewey, 2011) . The mapping was done against GRCh38 genome based on Ensembl's gene annotation version 83, with Bowtie2-V2.1.0(Langmead and Salzberg, 2012).
Variant calling on mapped reads was done using GATK3.7 tools: SplitNCigarReads with default parameters, HaplotypeCaller with default parameters with ploidy set to 10. Next, variant filtration was done by using SelectVariants with QD<2.0, FS>30.0, MQ<40.0, MQRankSum<-12.5, ReadPosRankSum<-8.0 for SNPs and QD<2.0, FS>30.0 and ReadPosRankSum<-20.0 for indels. Annotation was done with Ensembl’s Variant Effect Predictor v.83 against GRCh38, annotation v83.
Genome_build: GRCh38
Supplementary_files_format_and_content: A joint vcf file for all samples. A tab delimited txt file with TPM values for each sample

source_name: Brain

extract_protocol:
Tissue samples were obtained from Newcastle Brain Tissue Resource (NBTR). They were homogenized using Bullet Blender (Next Advance, Inc., NY, USA).  RNA and DNA were extracted from the same tissue with ZR-Duet DNA-RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA).
Libraries were prepared using SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian according to user manual guide

value: Postmortem Olfactory bulb

tag: disease

value: Healthy


title: Riboseq_RNA_APCdef_shEIF2B5_rep3

value: EtOH


title: Obesity 2

description: Gene expression data from adipose tissue in obese patient

source_name: Adipose tissue from obese patient 2

value: Visceral fat tissue


title: IP12 Sample32

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 1018dilution antiDSG3 antibody
Supplementary Table S7
32_15_S15_L001


title: IP11 Sample31

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 1018 dilution antiDSG3 antibody
Supplementary Table S7
31_14_S14_L001


title: Riboseq_RNA_APCdef_shCTR_rep3

value: human colorectal cancer cell line


title: Riboseq_Ribo_APCres_shEIF2B5_rep3

description:
processed data file:
Riboseq_RPF_SW480.txt

extract_protocol:
Ribosomal profiling (Ribo, RPF=ribosome protected fragments) and corresponding RNA-seq were performed using the TruSeq Ribo Profile for Mammalian kit from Illumina according to manufacturer's instructions.
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) including on-column digestion of DNA. Poly-A+ RNA was purified from total RNA with the NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB).

value: Dox


title: IP10 Sample30

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 1018 dilution antiDSG3 antibody
Supplementary Table S7
30_13_S13_L001


title: IP09 Sample29

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 1012 dilution antiDSG3 antibody
Supplementary Table S7
29_11_S11_L001


title: Patient37 RNA-Seq

value: Alzheimer's Disease


title: Riboseq_Ribo_APCres_shCTR_rep3


title: Riboseq_Ribo_APCdef_shEIF2B5_rep3


title: IP07 Sample27

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 1012 dilution antiDSG3 antibody
Supplementary Table S7
27_9_S9_L001


title: IP06 Sample26

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 108 dilution antiDSG3 antibody
Supplementary Table S7
26_7_S7_L001


title: Patient35 RNA-Seq


title: IP05 Sample25

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 108 dilution antiDSG3 antibody
Supplementary Table S7
25_6_S6_L001


title: Obesity 1

source_name: Adipose tissue from obese patient 1


title: Riboseq_Ribo_APCdef_shCTR_rep3


title: IP04 Sample24

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 108 dilution antiDSG3 antibody
Supplementary Table S7
24_5_S5_L001


title: Patient34 RNA-Seq


title: Healthy40 RNA-Seq


title: negative control for IP01 Sample33

description:
4Oligos(Oligo71-74) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 104 dilution human serum
Supplementary Table S7
33_17_S17_L001

value: negative control for IP01


title: IP03 Sample23

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 108pM DSG3,103pM HaloTag : 104 dilution antiDSG3 antibody
Supplementary Table S7
23_3_S3_L001


title: IP02 Sample22

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 104 dilution antiDSG3 antibody
Supplementary Table S7
22_2_S2_L001


title: Riboseq_RNA_APCres_shEIF2B5_rep2

description:
processed data file:
Riboseq_RNA_SW480_rep2.txt


title: Healthy38 RNA-Seq


title: IP01 Sample21

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 540pM DSG3, 515pM HaloTag : 104 dilution antiDSG3 antibody
Supplementary Table S7
21_1_S1_L001


title: Patient33 RNA-Seq


title: Riboseq_RNA_APCres_shCTR_rep2


title: Patient32 RNA-Seq


title: PRSRRS02 Sample20

description:
32Oligos(01-04, 17-28,31-38,71-78) Supplementary Table S1
PRSRRS assay
Supplementary Table S3
20_3_S3_L001

source_name: 32Oligos_Figure 3B


title: IP08 Sample28

description:
4Oligos(Oligo59-62) Supplementary Table S1
Desmoglein 3 (DSG3) barcode immunoprecipitation. 216pM DSG3, 206pM HaloTag : 1012 dilution antiDSG3 antibody
Supplementary Table S7
28_10_S10_L001


title: Riboseq_RNA_APCdef_shEIF2B5_rep2


title: PRSRRS01 Sample19

description:
32Oligos(Oligo31-38,47-62,71-78) Supplementary Table S1
PRSRRS assay
Supplementary Table S3
19_1_S1_L001


title: Healthy36 RNA-Seq


title: Patient31 RNA-Seq


title: Obesity 3

description: Gene expression data from adipose tissue in obese patient

source_name: Adipose tissue from obese patient 3


title: 10^8 dilution of NL-JUN-Oligo03 Sample17

description:
Oligo03 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
17_53_S33_L001

source_name: Oligo03_Figure 2D (green)

value: 108 dilution of NL-JUN-Oligo03


title: Healthy30 RNA-Seq


title: 10^9 dilution of NL-JUN-Oligo03 Sample18

description:
Oligo03 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
18_54_S34_L001

value: 109 dilution of NL-JUN-Oligo03


title: 10^7 dilution of NL-JUN-Oligo03 Sample16

description:
Oligo03 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
16_52_S32_L001

value: 107 dilution of NL-JUN-Oligo03


title: Riboseq_Ribo_APCres_shEIF2B5_rep2

description:
processed data file:
Riboseq_RPF_SW480.txt


title: 10^6 dilution of NL-JUN-Oligo03 Sample15

description:
Oligo03 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
15_47_S27_L001

value: 106 dilution of NL-JUN-Oligo03


title: Patient29 RNA-Seq


title: Riboseq_RNA_APCdef_shCTR_rep2


title: 10^4 dilution of NL-JUN-Oligo03 Sample13

description:
Oligo03 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
13_45_S25_L001

value: 104 dilution of NL-JUN-Oligo03


title: Riboseq_Ribo_APCres_shCTR_rep2

value: shCTR


title: 10^5 dilution of NL-JUN-Oligo03 Sample14

description:
Oligo03 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
14_46_S26_L001

value: 105 dilution of NL-JUN-Oligo03


title: Healthy28 RNA-Seq


title: Healthy27 RNA-Seq


title: 10^8 dilution of NL-FOS-Oligo06 Sample11

description:
Oligo06 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
11_48_S48_L001

source_name: Oligo06_Figure 2D (red)

value: 108 dilution of NL-FOS-Oligo06


title: 10^5 dilution of NL-FOS-Oligo06 Sample08

description:
Oligo06 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
08_45_S45_L001

value: 105 dilution of NL-FOS-Oligo06


title: Riboseq_Ribo_APCdef_shCTR_rep2


title: Healthy26 RNA-Seq

value: Postmortem Olfactory bulb


title: Riboseq_Ribo_APCdef_shEIF2B5_rep2


title: 10^6 dilution of NL-FOS-Oligo06 Sample09

description:
Oligo06 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
09_46_S46_L001

value: 106 dilution of NL-FOS-Oligo06


title: Riboseq_RNA_APCres_shEIF2B5_rep1

description:
processed data file:
Riboseq_RNA_SW480_rep1.txt


title: 10^9 dilution of NL-Oligo01 Sample06

description:
Oligo01 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
06_50_S30_L001

source_name: Oligo01_Figure 2D (blue)

value: 109 dilution of NL-Oligo01


title: Patient25 RNA-Seq


title: 10^8 dilution of NL-Oligo01 Sample05

description:
Oligo01 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
05_49_S29_L001

value: 108 dilution of NL-Oligo01


title: 10^7 dilution of NL-Oligo01 Sample04

description:
Oligo01 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
04_44_S24_L001

value: 107 dilution of NL-Oligo01


title: Riboseq_RNA_APCres_shCTR_rep1

value: human colorectal cancer cell line

value: Dox


title: Healthy24 RNA-Seq

value: Healthy


title: Riboseq_RNA_APCdef_shEIF2B5_rep1

value: EtOH


title: Healthy22 RNA-Seq


title: 10^5 dilution of NL-Oligo01 Sample02

description:
Oligo01 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
02_42_S22_L001

value: 105 dilution of NL-Oligo01


title: 10^6 dilution of NL-Oligo01 Sample03

description:
Oligo01 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
03_43_S23_L001

value: 106 dilution of NL-Oligo01


title: Riboseq_RNA_APCdef_shCTR_rep1


title: 10^4 dilution of NL-Oligo01 Sample01

description:
Oligo01 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
01_41_S21_L001

value: 104 dilution of NL-Oligo01


title: 10^7 dilution of NL-FOS-Oligo06 Sample10

description:
Oligo06 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
10_47_S47_L001

value: 107 dilution of NL-FOS-Oligo06


title: Patient21 RNA-Seq

value: Alzheimer's Disease


title: T3-3

city: Zhengzhou

first: Gaopeng

last: Yuan

state: Henan

address: Weilai Road Nanduan

institute: CAAS

data_processing:
BGISEQ-500 software used for basecalling.
The original sequencing data contain reads with low quality, joint contamination and high unknown base N content, which should be removed before data analysis to ensure the reliability of the results.
gene expression levels were calculated by FPKM (fragments per kilobase million)
Genome_build: GDDH13
Supplementary_files_format_and_content: final processed data

organism: Malus domestica

source_name: fruit skin

growth_protocol: The apples were bagged at DAF 20 , 100-150 exposed fruits per tree were selected for the control group (short for CK), and 50 well fruits were bagged with light impermeable double layer (the outer layer is yellow outside and black inside, and the inner layer is red) paper bagsfor the treatment group (short for T).

extract_protocol:
Skins were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.RNA was extracted from 200 mg fruit skin using the RNeasy Plant Mini Kit (Tiangen, China) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISEQ-500

treatment_protocol: All three fruit of each sample were peeled and mixed according to Legay et. al., then directly flash-frozen in liquid nitrogen and stored at -80℃ immediately prior to RNA and protein extraction.

value: fruit

tag: developmental stage

value: day after flowering

tag: time


title: Patient10 RNA-Seq

description: Sample 20


title: Riboseq_Ribo_APCres_shEIF2B5_rep1


title: Riboseq_Ribo_APCres_shCTR_rep1

value: shCTR


title: T3-1


title: 10^4 dilution of NL-FOS-Oligo06 Sample07

description:
Oligo06 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
07_44_S44_L001

value: 104 dilution of NL-FOS-Oligo06


title: T2-1


title: T2-2


title: 10^9 dilution of NL-FOS-Oligo06 Sample12

description:
Oligo06 Supplementary Table S1
the dynamic range of HaloTag barcode assay
Supplementary Table S6
12_49_S49_L001

value: 109 dilution of NL-FOS-Oligo06


title: T1-3


title: Patient8 RNA-Seq

description: Sample 18

value: Postmortem Olfactory bulb


title: Riboseq_Ribo_APCdef_shEIF2B5_rep1

description:
processed data file:
Riboseq_RPF_SW480.txt

extract_protocol:
Ribosomal profiling (Ribo, RPF=ribosome-protected fragment) and corresponding RNA-seq were performed using the TruSeq Ribo Profile for Mammalian kit from Illumina according to manufacturer's instructions.
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) including on-column digestion of DNA. Poly-A+ RNA was purified from total RNA with the NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB).


title: Riboseq_Ribo_APCdef_shCTR_rep1

treatment_protocol: SW480TetOnAPC cells were lentivirally infected with an shRNA targeting EIF2B5 or non-specific control (shLuciferase). Cells were treated with 0.5 µg/ml doxycycline or ethanol for 96 hours to restore APC expression.


title: Patient7 RNA-Seq

description: Sample 17


title: T1-1


title: T1-2


title: CK3-3


title: Cyclo Rep2

city: Thiverval Grignon

first: Julie

last: Gervais

address: Avenue Lucien Brétignières

department: BIOGER

country: France

institute: INRA

data_processing:
The sofwtware CLC worckbench v8.5.1 (Qiagen, Venlo, Netherlands) was used for data processing.
Sequenced reads were trimmed with the following parameters: ambiguous limit: 2, quality limit: 0.05, maximum number of nucleotides in reads: 50, minimum number of nucleotides in reads: 15. Short reads were discarded.
Reads were mapped on the genomes of L. maculans and B. napus with the following parameters: maximum number of mismatches allowed: 2, minimum lenght fraction: 0.80, Minim fraction of similarity: 0.8, unspecific match limit: 30
Gene expression was normalized using the DESeq2 package (Love et al., 2014)
Genome_build: Leptosphaeria maculans JN3 (Rouxel et al., 2011)
Supplementary_files_format_and_content: Text files include raw and normalized (with DESeq2) values for each fungal gene.

organism: Plenodomus lingam

source_name: with cycloheximide

growth_protocol: Liquid MMII medium supplemented or not with cycloheximide was inoculated with 10^8 conidia of the v23.1.2 isolate of L. maculans. Incubation lasted for 3-4 days.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen,Cergy Pontoise, France) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs, Ipswich, MA, U.S.A.).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: mycelia

value: with cycloheximide


title: CK3-2


title: CK3-1


title: T3-2


title: Patient6 RNA-Seq

description: Sample 16


title: CK2-3


title: CK2-2


title: T2-3


title: CK1-3


title: CK2-1


title: Patient4 RNA-Seq

description: Sample 14


title: Patient5 RNA-Seq

description: Sample 15


title: Patient9 RNA-Seq

description: Sample 19


title: Myc Rep2

source_name: without cycloheximide

value: without cycloheximide


title: Patient3 RNA-Seq

description: Sample 13


title: CK1-2


title: CK1-1


title: Baboon 24 hr RPE 4

description:
THoa-RPE3_PR8-2_S7
X24hr4Aligned.out.bam

data_processing:
Raw files were aligned using RNA-STAR
Rsubread's featurcounts was used to generate read counts
edgeR was used for DE
R enviroment was used to analyze data
Genome_build: GRCm38.p6 and Panu_3.0
Supplementary_files_format_and_content: csv, raw counts from Rsubread

organism: Papio anubis

source_name: Baboon RPE/choroid

extract_protocol:
Retina/RPE was isolated, stored at 4 degress in RNA later or RNA protect, respectively, and RNA was harvested miRNAeasy micro.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Olive Baboon

value: Female

value: 11 years

tag: pmi interval

value: 24 hr

value: RPE/choroid


title: Patient2 RNA-Seq

description: Sample 12


title: III_QMY3_Treated

city: Debrecen

first: Krisztina

last: Szabó

address: Egyetem tér

department: Medical Chemistry

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of sequencing data was performed using FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
STAR RNA-Seq aligner was used to map the sequenced reads to the reference genome and generate BAM files
DESeq algorithm was used to obtain normalized gene expression values (StrandNGS software)
Gene expression differences between treated and control groups were compared by moderated T-test; Benjamini-Hochberg False Discovery Rate was used for multiple testing correction.
Genome_build: C. albicans SC5314 (C_albicans_SC5314/ Assembly22 genome version, downloaded from www.candidagenome.org)
Supplementary_files_format_and_content: Exel file includes RPKM and fold change values

organism: Candida albicans

source_name: fungal cells

growth_protocol: The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 37ºC without shaking  for 18 hours then diluted to OD640 0.1 value in 20 mL of YPD and incubated at 37ºC with 140 rpm shaking.

extract_protocol:
Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent (Chomczynski BioTechniques. 1993; 15:536–7.) and glass beads. RNA concentration and purity were determined using NanoDrop (Thermo Scientific) and  by Bioanalyser (Agilent) using Eukaryotic Total RNA Nano Kit according to the manufacturer's protocol.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the eluted mRNAs were fragmented at 94°C. First strand cDNA was generated by random priming reverse transcription; double stranded cDNA was generated in a second strand synthesis step. After repairing ends, A-tailing and adapter ligation steps, adapter-ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated. Sequencing libraries were normalized to the same molar concentration and pooled together. Library pool was sequenced on NextSeq500 instrument (Illumina, San Diego, CA, USA) generating single read 75bp-long sequencing reads. Fastq files were generated automatically after the sequencing run by Illumina BaseSpace.

treatment_protocol: Following 4 hours incubation time YPD medium was supplemented with a final concentration of 0.4 mM tert-butyl-hydroperoxide (tBOOH) and fungal cells were collected 1 hours following tBOOH exposure by centrifugation (10 min, RCF=7750g, 4°C). The cells were washed two times with phosphate-buffered saline and stored at -70°C until use.

value: wild type

value: fungal cells


title: Patient1 RNA-Seq

description: Sample 11

value: Alzheimer's Disease


title: Baboon 24 hr RPE 3

description:
THoa-RPE3_PR8-1_S6
X24hr3Aligned.out.bam


title: III_QMY3_CTRL


title: Baboon 24 hr RPE 1

description:
THoa-RPE3_PR7-1_S4
X24hr1Aligned.out.bam


title: Baboon 6 hr RPE 4

description:
THoa-RPE3_PR6-2_S3
X6hr4Aligned.out.bam

value: 6 hr


title: III_KO3_Treated

value: mutant type


title: Healthy10 RNA-Seq

description: Sample 10

value: Healthy


title: Cyclo Rep1

tag: treatment


title: III_KO3_CTRL


title: Baboon 6 hr RPE 3

description:
THoa-RPE3_PR6-1_S2
X6hr3Aligned.out.bam


title: Healthy9 RNA-Seq

description: Sample 9


title: Baboon 6 hr RPE 1

description:
THoa-RPE3_PR5-1_S9
X6hr1Aligned.out.bam


title: II_QMY2_Treated


title: Healthy8 RNA-Seq

description: Sample 8


title: Baboon 3 h RPE 5

description:
THoa-RPE3_PR9-2_S9
X3hr5Aligned.out.bam

value: 3 h


title: Myc Rep1


title: Baboon 3 h RPE 3

description:
THoa-RPE3_PR4-1_S7
X3hr3Aligned.out.bam


title: II_QMY2_CTRL


title: Baboon 3 h RPE 2

description:
THoa-RPE3_PR3-2_S6
X3hr2Aligned.out.bam


title: II_KO2_Treated


title: Healthy6 RNA-Seq

description: Sample 6


title: Healthy7 RNA-Seq

description: Sample 7


title: II_KO2_CTRL


title: Healthy5 RNA-Seq

description: Sample 5


title: Baboon 0 h RPE 5

description:
THoa-RPE3_PR9-1_S8
X0hr5Aligned.out.bam

value: 0 h


title: Baboon 24 hr RPE 2

description:
THoa-RPE3_PR7-2_S5
X24hr2Aligned.out.bam


title: Baboon 0 h RPE 2

description:
THoa-RPE3_PR1-2_S2
X0hr2Aligned.out.bam


title: Baboon 0 h RPE 3

description:
THoa-RPE3_PR2-1_S3
X0hr3Aligned.out.bam


title: Healthy4 RNA-Seq

description: Sample 4

value: Postmortem Olfactory bulb


title: Baboon 0 h RPE 1

description:
THoa-RPE3_PR1-1_S1
X0hr1Aligned.out.bam


title: Baboon 24 hr retina 4

description:
BCla-8_2PRRet_S14
Ret24Hr4Aligned.out.bam

source_name: Baboon retina

value: retina


title: I_QMY1_Treated


title: Baboon 6 hr RPE 2

description:
THoa-RPE3_PR5-2_S1
X6hr2Aligned.out.bam


title: Baboon 0 h RPE 4

description:
THoa-RPE3_PR2-2_S4
X0hr4Aligned.out.bam


title: Baboon 24 hr retina 3

description:
BCla-8_1PRRet_S13
Ret24Hr3Aligned.out.bam


title: Baboon 3 h RPE 4

description:
THoa-RPE3_PR4-2_S8
X3hr4Aligned.out.bam


title: I_KO1_Treated


title: Healthy3 RNA-Seq

description: Sample 3


title: Healthy1 RNA-Seq

description: Sample 1


title: Baboon 3 h RPE 1

description:
THoa-RPE3_PR3-1_S5
X3hr1Aligned.out.bam


title: Baboon 24 hr retina 2

description:
BCla-7_2PRRet_S12
Ret24Hr2Aligned.out.bam


title: I_KO1_CTRL


title: Baboon 24 hr retina 1

description:
BCla-7_1PRRet_S11
Ret24Hr1Aligned.out.bam


title: Baboon 6 hr retina 4

description:
BCla-6_2PRRet_S10
Ret6Hr4Aligned.out.bam


title: Baboon 6 hr retina 1

description:
BCla-5_1PRRet_S7
Ret6Hr1Aligned.out.bam


title: I_QMY1_CTRL


title: Zfp281_sh10_Myc

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
ChipSeq samples were aligned using Bowtie2 (v2.2.5)  allowing uniquely mapping reads only
Peak calling was performed with MACS2 (v2.1.1) and filtered at FDR < 5 (0.05)
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: murine embryonic stem cells

growth_protocol: Mouse embryonic stem cells V6.5 were cultured on irradiated mouse embryonic fibroblast (MEF) feeder layers in 0.1% gelatin-coated tissue culture flask.

extract_protocol:
For ChIP-Seq, 5×10^7 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's ChIP-Seq sample prep kit (0801-0303).
NEBNext® DNA Library Prep Master Mix Set for Illumina

value: C57BL/6 (female) x 129/S (male)

value: murine embryonic stem cells

tag: chip antibody

value: C-Myc(N-262) (Santa Cruz, catalog# sc-764, lot# 12613)


title: Baboon 3 h retina 4

description:
BCla-9_2PRRet_S2
Ret3Hr4Aligned.out.bam

value: Olive Baboon

value: Female


title: Zfp281_sh10_input

tag: cell type


title: Baboon 3 h retina 3

description:
BCla-4_2PRRet_S6
Ret3Hr3Aligned.out.bam

value: 11 years


title: Baboon 3 h retina 2

description:
BCla-3_2PRRet_S5
Ret3Hr2Aligned.out.bam


title: Healthy2 RNA-Seq

description: Sample 2


title: Baboon 3 h retina 1

description:
BCla-3_1PRRet_S4
Ret3Hr1Aligned.out.bam


title: MYC

data_processing:
ChipSeq samples were aligned using Bowtie2 (v2.2.5)  allowing uniquely mapping reads only
Peak calling was performed with MACS2 (v2.1.1) and filtered at FDR < 5 (0.05)
Genome_build: mm9

growth_protocol: Mouse embryonic stem cells V6.5 were cultured on irradiated mouse embryonic fibroblast (MEF) feeder layers in 0.1% gelatin-coated tissue culture flask. Cells were

extract_protocol:
For ChIP-Seq, 5×107 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's ChIP-Seq sample prep kit (0801-0303).
NEBNext® DNA Library Prep Master Mix Set for Illumina

value: c-Myc Antibody (N-262)

tag: chip antibody info.


title: ChIP-seq of V6.5 SHC Input in mESC

value: mouse embryonic stem cells


title: Baboon 0 h retina 3

description:
BCla-2_1PRRet_S3
Ret0Hr3Aligned.out.bam

tag: gender


title: Baboon 6 hr retina 3

description:
BCla-6_1PRRet_S9
Ret6Hr3Aligned.out.bam

tag: age


title: Baboon 0 h retina 1

description:
BCla-1_1PRRet_S1
Ret0Hr1Aligned.out.bam


title: Baboon 0 h retina 4

description:
BCla-9_1PRRet_S1
Ret0Hr4Aligned.out.bam


title: Baboon 6 hr retina 2

description:
BCla-5_2PRRet_S8
Ret6Hr2Aligned.out.bam


title: Vi_1_pre: Patient 11 before splenectomy

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit

scan_protocol: Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)

data_processing: Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library.  The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Data was quantile normalized followed by log2 transform.  Signals from probes measuring same ncRNA were averaged.

source_name: peripheral blood leukocytes

label_protocol: Labbeling was done according to Nimblegen one color DNA Labeling kit.

extract_protocol: Total RNA extracted using Total RNA Purification Kit from Norgen Biotek corp following manufacturer's instructions

value: peripheral blood

tag: surgical indication

value: microsphercytosis

tag: total/partial resection

value: total

tag: Sex

value: female

tag: surgical approach

value: robotic


title: NB-CTRL, rep3

city: Louisv

first: Juw

middle: Won

last: Park

state: KY

address: 213 Duthie Center

department: CECS

institute: University of Louisville

description: Non-behavioral

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 84) then rn6 whole genome using STAR aligner 2.5.4b with parameters  --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --out  SAMstrandField intronMotif
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.1 with uniquely and properly mapped pairs.
Genome_build: rn6
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample.

organism: Rattus norvegicus

source_name: male Sprague Dawley Non-behavioral

extract_protocol:
Total RNA was isolated from amygdala using a Qiagen miRNA easy micro kit (Germantown, MD) which is specialized for isolation of RNA from lipid rich tissue (n=3). Each RNA sample containing 1 µg of RNA was used for poly A selected RNA-seq library preparation using the NEB Ultra-Directional RNA Library Prep Kit for Illumina, Cat# E7420.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

tag: tissue

value: amygdala

value: postnatal day 38

value: male


title: SMC_2_post: Patient 10 after splenectomy

value: immune thrombocytopenic purpura

value: laparoscopic


title: Si29_2_post: Patient 9 after splenectomy-1


title: Baboon 0 h retina 2

last: Kallestad

address: 829 Health Sciences Rd

institute: University of California Irvine

description:
BCla-1_2PRRet_S2
Ret0Hr2Aligned.out.bam

value: 0 h

value: retina


title: Si29_1_pre: Patient 9 before splenectomy


title: PM_3_post: Patient 8 after splenectomy

value: hypersplenism  of unkown cause

value: open


title: Si29_3_post: Patient 9 after splenectomy-2


title: HSR007_WT_Stim_rep2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: HSR007_1180667_ClariomSmouse.rma-gene-full-Signal

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: WT_Stim_CD4+CD25+ Tregs

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Lymphocytes were enriched using CD4 MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions, and then stained and sorted for CD25+CD4+ Tregs.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain background

tag: genotype/variation

value: WT

value: CD4+CD25+ Tregs

value: stimulated


title: HSR008_RagAB_KO_Stim_rep2

description: HSR008_1180668_ClariomSmouse.rma-gene-full-Signal

source_name: RagAB_KO_Stim_CD4+CD25+ Tregs

value: RagAB KO


title: NB-CTRL, rep2

description: Non-behavioral


title: Ni_2_post: Patient 7 after splenectomy

value: peripheral blood

value: total


title: B-CTRL, rep3

description: Behavioral Testing

source_name: male Sprague Dawley Behavioral Testing


title: DDF_2_post: Patient 6 after splenectomy

value: thalassemia major


title: Ni_1_pre: Patient 7 before splenectomy


title: HSR003_WT_Unstim_rep2

description: HSR003_1180663_ClariomSmouse.rma-gene-full-Signal

source_name: WT_Unstim_CD4+CD25+ Tregs

value: unstimulated


title: HSR002_WT_Unstim_rep1

description: HSR002_1180662_ClariomSmouse.rma-gene-full-Signal


title: B-CTRL, rep2

description: Behavioral Testing

value: Sprague Dawley

value: amygdala


title: HSR004_RagAB_KO_Unstim_rep2

description: HSR004_1180664_ClariomSmouse.rma-gene-full-Signal

source_name: RagAB_KO_Unstim_CD4+CD25+ Tregs


title: Sr_3_post: Patient 5 after splenectomy

value: female


title: DDF_1_pre: Patient 6 before splenectomy

value: male


title: HSR001_RagAB_KO_Unstim_rep1

description: HSR001_1180661_ClariomSmouse.rma-gene-full-Signal


title: HSR005_RagAB_KO_Stim_rep1

description: HSR005_1180665_ClariomSmouse.rma-gene-full-Signal


title: Rheb1/2_KO_Stim_rep3

description: NMC045_1604979_ClariomSmouse.rma-gene-full-Signal

source_name: Rheb1/2_KO_Stim_CD4+CD25+ Tregs

value: Rheb1/2 KO


title: Rheb1/2_KO_Stim_rep1

description: NMC043_1604977_ClariomSmouse.rma-gene-full-Signal


title: Sr_1_pre: Patient 5 before splenectomy

value: immune thrombocytopenic purpura

value: laparoscopic


title: WT_Stim_rep3

description: NMC042_1604976_ClariomSmouse.rma-gene-full-Signal


title: NB-CTRL, rep1

description: Non-behavioral

value: postnatal day 38


title: HSR006_WT_Stim_rep1

description: HSR006_1180666_ClariomSmouse.rma-gene-full-Signal


title: Se_2_post: Patient 4 after splenectomy

value: hydatid cyst of the spleen

value: open


title: B-CTRL, rep1

description: Behavioral Testing


title: EE_scRNA-seq

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

description:
G101_1_TACTCT_L003
G101_2_CCTGTG_L003
G101_3_GGACAC_L003
G101_4_ATGAGA_L003

data_processing:
cellranger V2.0
Genome_build: BDGP6
Supplementary_files_format_and_content: cellranger V2.0 outputs

source_name: FACS sorted Enteroendocrine cell

growth_protocol: Flies were cultured on standard media with yeast paste added to the food surface, and the culture temperature was 25℃.

extract_protocol:
RNA and library was prepared by following the manufacturer’s instructions of 10X genomics scRNA-seq
Libraries were prepared for sequencing using standard Illumina protocols
10X genomics single cell RNA-sequencing

value: intestine

value: adult stage 5-7 days old

tag: genotype


title: Se_1_pre: Patient 4 before splenectomy


title: M_1_pre: Patient 3 before splenectomy


title: B_1_pre: Patient 2 before splenectomy

value: microsphercytosis

value: subtotal

value: robotic


title: B_3_post: Patient 2 after splenectomy

value: peripheral blood


title: AN_1_pre: Patient 1 before splenectomy


title: WT_Stim_rep2

description: NMC041_1604975_ClariomSmouse.rma-gene-full-Signal

value: WT

value: CD4+CD25+ Tregs

value: unstimulated


title: M_2_post: Patient 3 after splenectomy

value: total

value: female


title: Rheb1/2_KO_Stim_rep2

description: NMC044_1604978_ClariomSmouse.rma-gene-full-Signal

value: Rheb1/2 KO

value: stimulated


title: WT_Stim_rep1

description: NMC040_1604974_ClariomSmouse.rma-gene-full-Signal


title: Rheb1/2_KO_Unstim_rep2

description: NMC038_1604972_ClariomSmouse.rma-gene-full-Signal

source_name: Rheb1/2_KO_Unstim_CD4+CD25+ Tregs


title: Vi_2_post: Patient 11 after splenectomy


title: Rheb1/2_KO_Unstim_rep1

description: NMC037_1604971_ClariomSmouse.rma-gene-full-Signal


title: SMC_1_pre: Patient 10 before splenectomy

value: immune thrombocytopenic purpura

value: laparoscopic


title: Rheb1/2_KO_Unstim_rep3

description: NMC039_1604973_ClariomSmouse.rma-gene-full-Signal


title: Muscle of ADCK2(+/-) mutant mouse - rep 5

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

country: Spain

institute: Universidad Pablo de Olavide

description:
replicate 5
M-ADCK2_5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse gastronomius muscle

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed by RNA electrophoresis and with Agilent Bioanalyser.

value: ADCK2(+/-) mutant

value: 3 year old

value: muscle


title: TCR_PD8

city: Stanford

first: Olivia

last: Leventhal

state: California (CA)

address: 1201 Welch Road, rm p220

department: Neurology

institute: Stanford University

data_processing:
Library strategy: single cell TCR-seq
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
TCR-seq reads were mapped alligned to the GRCh38 2.0.0 vdj genome assembly available from 10X Genomics using cellranger count version 3.0.2
T cell receptor sequences were generated using cellranger vdj version 3.0.2
Genome_build: GRCh38 vdj 2.0.0
Supplementary_files_format_and_content: two files for each sample; one file that indicates clonotypes and one file that has the sequence for each cell barcode

source_name: cerebrospinal fluid derived cells

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD Biosciences). RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' V(D)J Kit.

value: cerebrospinal fluid

value: T cells

tag: diagnosis

value: PD


title: Naturally restored secondary forests_rep11

type: genomic

first: Yun

last: Wang

address: Shuangqing Road 18th, Haidian District

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

hyb_protocol: The labeled DNA was suspended in 120 µl hybridization solution (50% formamide, 3 × SSC, 10 µg of unlabeled herring sperm DNA (Promega, Madison, WI), and 0.1% SDS. The mix was kept at 95°C for 5 min and kept at 50°C until deposited onto a microarray. Hybridizations were performed with a TECAN Hybridization Station HS4800 Pro (TECAN, US) (Xue et al. 2007) (K. Xue, M.M. Yuan, J.P. Xie, D. Li, Y. Qin, L. E. Hale, L. Wu, Y. Deng, Z. He, J. D. Van Nostrand, Y. Luo, J. M. Tiedje, J. Zhou. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio 7, 1-12 (2016)).

scan_protocol: The hybridized GeoChip 3.0 was scanned with a ScanArray 5000 (Perkin-Elmer, Wellesley, MA, USA) at 95% laser energy and 85% photomultiplier tube gain, and digitally analyzed using Imagene software (6.0 premium version, Biodiscovery, El Segundo, CA, USA)

data_processing: The data were processed as follows: (i) Probes flagged as 1 or 3 by ImaGene and probes with signal to noise ratio < 2.0 were removed; (ii) Data were normalized firstly within a slide，then among samples，and finally devided by the mean of the signal intensities of all probes; (iii) Probes appeared less than 3 times for each reforestation approach were deleted; (iv) Samples with probe numbers outside of mean ± (2 × standard error) were considered outliers (ARMP1, NRSF2, and NRSF7) and removed. In total, 14, 14, and 11 microarray replicates were obtained for ARSP, ARMP, and NRSF, respectively.

organism:
Bacteria
Archaea
Fungi
Viruses

source_name: Naturally restored secondary forests

label_protocol: The DNA was labeled by Cy5 as described (Xue et al. 2007). Firstly, the DNA was mixed with 20 μL random primers, denatured at 99.9 °C for 5 min, and chilled on ice. Secondly, the labeling master mix (2.5 μL dNTP (5 mM dAGC-TP, 2.5 mM dTTP), 1 μL Cy-5 dUTP (Amersham, Piscataway, NJ), 80 U of the large Klenow fragment (Invitrogen, Carlsbad, CA), and 2.5 μL water) were added, incubated at 37°C for 3 h, and then heated at 95 °C for 3 min. Thirdly, the labeled DNA was purified with the QIA quick purification kit (Qiagen, Valencia, CA), measured on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE), and then dried in a SpeedVac (ThermoSavant, Milford, MA) at 45 °C for 45 min (Xue et al. 2007). (K. Xue, M.M. Yuan, J.P. Xie, D. Li, Y. Qin, L. E. Hale, L. Wu, Y. Deng, Z. He, J. D. Van Nostrand, Y. Luo, J. M. Tiedje, J. Zhou. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio 7, 1-12 (2016)).

growth_protocol: Soil samples were collected from the top 10 cm in October 2008 and August, September 2009. Each sample was composition of fifteen soil cores (3.5 cm diameter). All samples were sieved through 2 mm sieves, and stored at -80 °C.

extract_protocol: Soil DNA was extracted by phenol/chloroform method with Al2(SO4)3 pretreatment (Peršoh et al. 2008). Firstly, 0.5 g soil was washed with an excess Al2(SO4)3 (0.2 M) which was subsequently removed with a 4 M NaOH solution. Secondly, DNA and protein were extracted from soil with Tris-HCl buffer (0.4 M LiCl, 100 mM Tris–HCl, 120 mM EDTA, pH 8) and 0.5 g glass beads by glass beading. Thirdly, DNA and protein were separated with phenol:chloroform:alcohol (25:24:1) and chloroform:isoamyl alcohol (24:1), and the supernatant was washed with chloroform overnight. Fourthly, DNA was precipitated twicely with 70% cold ethanol at 13000 rpm for 60 min and 15 min, respectively (Peršoh et al. 2008). (D. Peršoh, S. Theuerl, F. Buscot, G. Rambold, Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J. Microbiol. Meth. 75, 19-24 (2008)).

treatment_protocol: The forests have been restored for about tweenty years. The restored forests were naturally restored secondary forests (NRSF), artificial reforestation with native Masson pine (Pinus massoniana Lamb.) (ARMP), and introduced slash pine (Pinus elliottii Engelm.) plantations (ARSP). For each forest restoration method, 15 plots (500 m × 500 m) were studied. Fifteen soil cores were collected from each plot, and then combined to create a composite sample.

tag: site

value: Guangxi Province Guilin City

tag: dominant tree species

value: Fagus longipetiolata Seem., Schima superba Gardn. et Champ., Castanopsis hystrix Miq., and Diospyros kaki Thunb


title: Naturally restored secondary forests_rep9


title: Artificial restored Masson pine plantations_rep1 [ARMP1]

source_name: Artificially restored Masson pine plantations

value: Hunan Province Hengyang County

tag: dominant species

value: Dominant tree species: Pinus massoniana Lamb.


title: Naturally restored secondary forests_rep7 [NRSF7]

value: Jiangxi Province Anfu County

value: Cinnamomum camphora L. and Cunninghamia lanceolata (Lamb.) Hook.


title: Naturally restored secondary forests_rep2 [NRSF2]

value: Liquidambar formosana Hance, Pinus massoniana Lamb., Castanopsis sclerophylla (Lindl.) Schott., and Quercus fabri Hance


title: Naturally restored secondary forests_rep8


title: Naturally restored secondary forests_rep10


title: TCR_HC17

value: HC


title: WT_Unstim_rep3

description: NMC036_1604970_ClariomSmouse.rma-gene-full-Signal

value: WT

value: CD4+CD25+ Tregs

tag: treatment

value: unstimulated


title: AN_2_post: Patient 1 after splenectomy

value: peripheral blood

value: microsphercytosis

value: subtotal

value: female

value: robotic


title: TCR_PD7

value: cerebrospinal fluid

tag: cell type

value: T cells

value: PD


title: WT_Unstim_rep1

description: NMC034_1604968_ClariomSmouse.rma-gene-full-Signal


title: TCR_HC16


title: TCR_MCI7

value: MCI


title: TCR_AD9

value: AD


title: Muscle of ADCK2(+/-) mutant mouse - rep 1

description:
replicate 1
M-ADCK2_1

value: ADCK2(+/-) mutant

tag: strain

value: 3 year old

value: muscle


title: Naturally restored secondary forests_rep6

value: Jiangxi Province Anfu County

value: Cinnamomum camphora L. and Cunninghamia lanceolata (Lamb.) Hook.


title: 129S4/SvJae

city: Cambridge

first: Peter

last: Nicholls

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Two Affymetrix Mouse Diversity Genotyping Arrays were processed in the presence of 197 other arrays of the same design from two NCBI GEO datasets (GSE36409 and GSE61660). Calls were made with Affymetrix Power Tools version version 1.17.0 using the command. apt-probeset-genotype -o results_brlmm-p_all_dir_v7 -c MOUSEDIVm520650.CDF --a quant-norm.sketch=50000,pm-only,brlmm-p.CM=1.bins=100.mix=1.bic=2.HARD=3.SB=0.75.KX=0.2.KH=0.3.KXX=-0.1.KAH=-0.1.KHB=-0.1.transform=MVA.AAM=2.0.BBM=-2.0.AAV=0.06.BBV=0.06.ABV=0.06.copyqc=0.00000.wobble=0.05.CSepThr=4.CSepPen=0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.AAY=9.ABY=9.5.BBY=9.copytype=-1.clustertype=2.ocean=0.00001.MS=0.1 --read-models-brlmmp Mouse.models --summaries --chrX-probes Mouse.chrXprobes --chrY-probes Mouse.chrYprobes --special-snps Mouse.specialSNPs *.CEL . The command was taken from the Affymetrix mouse vignette at http://www.affymetrix.com/estore/support/developer/powertools/changelog/VIGNETTE-Mouse-WGSA-genotyping.html.affx . Array annotation files were downloaded from the Affymetrix website (http://www.affymetrix.com/Auth/support/downloads/library_files/mouse_diversity_analysis.zip) . All SNPs were filtered by maximum p-value (0.01) and calls that were homozygous but differed between samples.

source_name: Mouse ear

label_protocol: As per the manufacturer (Affymetrix)

extract_protocol: DNA isolation from mouse ear skin sample. Digestion overnight and DNA precipitation by Isopropanol. Sample clean-up by phenol/chloroform extraction and resuspended in 1xTE buffer.


title: 129S2/SvPasCrl